Re: [Rdkit-discuss] How to encode atomic contributions to logP (hydrophobicity) in MOL2 formatted charge slot?
Hi Jim, The biggest challenge here is likely to be the fact that the RKDit doesn't have a Mol2 writer. -greg On Tue, Nov 13, 2018 at 7:05 PM James T. Metz via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > RDkit Discussion Group, > > Given a set of small molecules as a SDF file, I would like to generate > a MOL2 > file where the atomic contributions to logP (hydrophobicity) from each > atom including > hydrogens have been calculated and are now encoded in the partial atomic > charge > "slot" in a MOL2 file. Is this possible using RDkit? > > I have found code that calculates the atomic contributions for the > Crippen > logP model and then generates a colorized 2D plot: > > >>> from rdkit.Chem import rdMolDescriptors > >>> contribs = rdMolDescriptors._CalcCrippenContribs(mol) > >>> fig = SimilarityMaps.GetSimilarityMapFromWeights(mol,[x for x,y in > contribs], ˓→colorMap='jet', contourLines=10) > > However, I would like to encode the atomic contributions as partial > atomic charges so > that this information can be written out in a MOL2 file for each atom. > > Does anyone have PYTHON/RDkit code to do this? Thank you. > > Regards, > Jim Metz > > > > > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] How to encode atomic contributions to logP (hydrophobicity) in MOL2 formatted charge slot?
On 14/11/2018 02:42, James T. Metz via Rdkit-discuss wrote:
RDkit Discussion Group,
Given a set of small molecules as a SDF file, I would like to
generate a MOL2
file where the atomic contributions to logP (hydrophobicity) from each
atom including
hydrogens have been calculated and are now encoded in the partial
atomic charge
"slot" in a MOL2 file. Is this possible using RDkit?
I have found code that calculates the atomic contributions for the
Crippen
logP model and then generates a colorized 2D plot:
from rdkit.Chem import rdMolDescriptors
contribs = rdMolDescriptors._CalcCrippenContribs(mol)
fig = SimilarityMaps.GetSimilarityMapFromWeights(mol,[x for x,y in
contribs], ˓→colorMap='jet', contourLines=10)
However, I would like to encode the atomic contributions as partial
atomic charges so
that this information can be written out in a MOL2 file for each atom.
Does anyone have PYTHON/RDkit code to do this? Thank you.
Hello,
I have this script that does part of the job:
---
#!/usr/bin/env python
from __future__ import print_function
import sys
import rdkit
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
if len(sys.argv) != 3:
print("usage: %s input.sdf output.pl" % sys.argv[0])
sys.exit(1)
sdf_input = sys.argv[1]
pl_output = sys.argv[2]
output = open(pl_output, 'w')
ok_count = 0
failed_count = 0
for mol in Chem.SDMolSupplier(sdf_input, removeHs = False):
if mol: # not null test
name = mol.GetProp("_Name")
cLogPcontribs = [x for x,y in
rdMolDescriptors._CalcCrippenContribs(mol)]
output.write("COMPND %s\n" % name)
conf = mol.GetConformer()
# atoms = mol.GetAtoms()
for i, contrib in enumerate(cLogPcontribs):
pos = conf.GetAtomPosition(i)
output.write("%f %f %f %f\n" % (pos.x, pos.y, pos.z,
contrib))
output.write("END\n")
ok_count += 1
else:
failed_count += 1
output.close()
print ("OK: %d - failed: %d\n" % (ok_count, failed_count))
---
Regards,
F.
Regards,
Jim Metz
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[Rdkit-discuss] How to encode atomic contributions to logP (hydrophobicity) in MOL2 formatted charge slot?
RDkit Discussion Group, Given a set of small molecules as a SDF file, I would like to generate a MOL2 file where the atomic contributions to logP (hydrophobicity) from each atom including hydrogens have been calculated and are now encoded in the partial atomic charge"slot" in a MOL2 file. Is this possible using RDkit? I have found code that calculates the atomic contributions for the Crippen logP model and then generates a colorized 2D plot: >>> from rdkit.Chem import rdMolDescriptors >>> contribs = >>> rdMolDescriptors._CalcCrippenContribs(mol) >>> fig = >>> SimilarityMaps.GetSimilarityMapFromWeights(mol,[x for x,y in >>> contribs],˓→colorMap='jet', contourLines=10) However, I would like to encode the atomic contributions as partial atomic charges so that this information can be written out in a MOL2 file for each atom. Does anyone have PYTHON/RDkit code to do this? Thank you. Regards, Jim Metz ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
